mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 512,643 | 0 | A | G | 50.4% | ‑6.4 / 172.0 | 135 | intergenic (+711/‑6052) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| * | USA300TCH1516_ALE | 111,512 | 0 | A | G | 27.6% | 209.4 / 81.8 | 135 | S194S (TCA→TCG) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 111,516 | 0 | C | A | 25.9% | 231.6 / 71.3 | 131 | Q196K (CAA→AAA) | USA300HOU_RS00520 | putative lipoprotein |
| Marginal new junction evidence (lowest skew 10 of 17 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000731 | = 4419 | 10 (1.720) | 14 (0.010) | 7/262 | 0.4 | 0.75% | intergenic (+384/‑81) | USA300HOU_pUSA300HOUMR0006/cadR | hypothetical protein/cadmium binding protein |
| ? | NC_012417 | = 1946 | 3682 (1.040) | intergenic (+179/+147) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein | |||||
| * | ? | CP000731 | = 4381 | 10 (1.720) | 8 (0.000) | 7/264 | 0.4 | 0.42% | intergenic (+346/‑119) | USA300HOU_pUSA300HOUMR0006/cadR | hypothetical protein/cadmium binding protein |
| ? | NC_012417 | = 1975 | 3828 (1.070) | intergenic (+208/+118) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein | |||||
| * | ? | CP000731 | 4334 = | 10 (1.720) | 8 (0.000) | 6/266 | 0.4 | 0.44% | intergenic (+299/‑166) | USA300HOU_pUSA300HOUMR0006/cadR | hypothetical protein/cadmium binding protein |
| ? | NC_012417 | 2027 = | 3605 (1.000) | intergenic (+260/+66) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein | |||||
| * | ? | CP000731 | 4294 = | 10 (1.720) | 12 (0.010) | 8/262 | 0.4 | 0.78% | intergenic (+259/‑206) | USA300HOU_pUSA300HOUMR0006/cadR | hypothetical protein/cadmium binding protein |
| ? | NC_012417 | 2073 = | 3033 (0.850) | intergenic (+306/+20) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein | |||||
| * | ? | CP000731 | = 1610 | 0 (0.000) | 14 (0.010) | 8/258 | 0.4 | 0.91% | intergenic (+395/‑461) | repA/USA300HOU_pUSA300HOUMR0003 | replication protein A/hypothetical protein |
| ? | NC_012417 | = 1047 | 3043 (0.870) | coding (148/192 nt) | USA300HOU_RS15665 | hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 68659 = | 76 (0.860) | 3 (0.040) | 3/242 | 10.5 | 4.4% | coding (775/852 nt) | USA300TCH1516_00061 | hypothetical protein |
| ? | USA300TCH1516_ALE | = 68655 | 63 (0.820) | coding (771/852 nt) | USA300TCH1516_00061 | hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | = 739800 | 74 (0.830) | 6 (0.070) | 3/252 | 10.8 | 7.6% | intergenic (+27/+561) | pitA_1/sle1_2 | Low‑affinity inorganic phosphate transporter 1/N‑acetylmuramoyl‑L‑alanine amidase sle1 |
| ? | USA300TCH1516_ALE | = 739823 | 79 (0.980) | intergenic (+50/+538) | pitA_1/sle1_2 | Low‑affinity inorganic phosphate transporter 1/N‑acetylmuramoyl‑L‑alanine amidase sle1 | |||||
| * | ? | USA300TCH1516_ALE | = 1262909 | 79 (0.890) | 3 (0.040) | 3/258 | 11.0 | 3.8% | intergenic (+34/‑193) | sucD/lytN_1 | Succinate‑‑CoA ligase [ADP‑forming] subunit alpha/putative cell wall hydrolase LytN |
| ? | USA300TCH1516_ALE | = 1262932 | 80 (0.970) | intergenic (+57/‑170) | sucD/lytN_1 | Succinate‑‑CoA ligase [ADP‑forming] subunit alpha/putative cell wall hydrolase LytN | |||||
| * | ? | USA300TCH1516_ALE | 613861 = | 122 (1.370) | 6 (0.070) +TGAGTCT |
3/264 | 11.2 | 4.9% | coding (2173/2844 nt) | sdrC | Serine‑aspartate repeat‑containing protein C |
| ? | USA300TCH1516_ALE | = 614081 | 121 (1.360) | coding (2393/2844 nt) | sdrC | Serine‑aspartate repeat‑containing protein C | |||||
| * | ? | USA300TCH1516_ALE | 52495 = | 65 (0.730) | 94 (1.070) +T |
3/276 | 11.5 | 58.0% | intergenic (+105/‑568) | USA300HOU_RS00215/USA300HOU_RS00220 | hypothetical protein/hypothetical protein |
| ? | USA300TCH1516_ALE | = 52988 | 72 (0.810) | intergenic (+598/‑75) | USA300HOU_RS00215/USA300HOU_RS00220 | hypothetical protein/hypothetical protein | |||||